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- PDB-4gpn: The crystal structure of 6-P-beta-D-Glucosidase (E375Q mutant) fr... -

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Basic information

Entry
Database: PDB / ID: 4gpn
TitleThe crystal structure of 6-P-beta-D-Glucosidase (E375Q mutant) from Streptococcus mutans UA150 in complex with Gentiobiose 6-phosphate.
Components6-phospho-beta-D-Glucosidase
KeywordsHYDROLASE / STRUCTURAL GENOMICS / PSI-BIOLOGY / PROTEIN STRUCTURE INITIATIVE / MIDWEST CENTER FOR STRUCTURAL GENOMICS / MCSG
Function / homology
Function and homology information


6-phospho-beta-glucosidase / 6-phospho-beta-glucosidase activity / : / carbohydrate catabolic process / cytosol
Similarity search - Function
Glycoside hydrolase family 1, active site / Glycosyl hydrolases family 1 active site. / Glycosyl hydrolases family 1, N-terminal conserved site / Glycosyl hydrolases family 1 N-terminal signature. / Glycosyl hydrolase family 1 / Glycoside hydrolase family 1 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
gentiobiose 6-phosphate / Phospho-beta-glucosidase
Similarity search - Component
Biological speciesStreptococcus mutans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.291 Å
AuthorsTan, K. / Michalska, K. / Li, H. / Jedrzejczak, R. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: Acta Crystallogr. D Biol. Crystallogr. / Year: 2013
Title: GH1-family 6-P-beta-glucosidases from human microbiome lactic acid bacteria.
Authors: Michalska, K. / Tan, K. / Li, H. / Hatzos-Skintges, C. / Bearden, J. / Babnigg, G. / Joachimiak, A.
History
DepositionAug 21, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 3, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.src_method / _entity.type / _struct_asym.entity_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 6-phospho-beta-D-Glucosidase
B: 6-phospho-beta-D-Glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,0086
Polymers110,9492
Non-polymers1,0594
Water2,594144
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4110 Å2
ΔGint-22 kcal/mol
Surface area33730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.220, 91.796, 94.225
Angle α, β, γ (deg.)90.00, 102.23, 90.00
Int Tables number4
Space group name H-MP1211
DetailsExperimentally unknown. THe chains A and B may form a dimer.

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Components

#1: Protein 6-phospho-beta-D-Glucosidase


Mass: 55474.359 Da / Num. of mol.: 2 / Mutation: E375Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus mutans (bacteria) / Strain: UA159 / Gene: bgl, SMU_1601 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic / References: UniProt: Q8DT00, 6-phospho-beta-glucosidase
#2: Polysaccharide 6-O-phosphono-beta-D-glucopyranose-(1-6)-beta-D-glucopyranose / gentiobiose 6-phosphate


Type: oligosaccharide, Oligosaccharide / Class: Substrate analog / Mass: 422.277 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: gentiobiose 6-phosphate
DescriptorTypeProgram
WURCS=2.0/2,2,1/[a2122h-1b_1-5][a2122h-1b_1-5_6*OPO/3O/3=O]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(6+1)][b-D-Glcp]{[(6+0)][P]{}}}LINUCSPDB-CARE
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.22 Å3/Da / Density % sol: 44.54 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2M NaCl, 0.1M Bis-Tris:HCl, 25% (w/v) PEG 3350, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97931 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 5, 2012 / Details: Mirror
RadiationMonochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 2.291→46 Å / Num. all: 43091 / Num. obs: 43091 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rmerge(I) obs: 0.122 / Net I/σ(I): 13.7
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.652 / Mean I/σ(I) obs: 1.7 / % possible all: 96.4

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
MOLREPphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3PN8

3pn8


Resolution: 2.291→46 Å / SU ML: 0.65 / σ(F): 1.34 / Phase error: 28.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2389 2162 5.02 %
Rwork0.1768 --
obs0.18 43064 98.57 %
all-43064 -
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.351 Å2 / ksol: 0.32 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.4886 Å2-0 Å211.9838 Å2
2---9.2527 Å2-0 Å2
3---7.764 Å2
Refinement stepCycle: LAST / Resolution: 2.291→46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7791 0 68 144 8003
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0088120
X-RAY DIFFRACTIONf_angle_d1.01611006
X-RAY DIFFRACTIONf_dihedral_angle_d14.4142922
X-RAY DIFFRACTIONf_chiral_restr0.0681109
X-RAY DIFFRACTIONf_plane_restr0.0041422
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2907-2.3440.36481260.30312445X-RAY DIFFRACTION88
2.344-2.40260.3631500.26712684X-RAY DIFFRACTION98
2.4026-2.46750.30611330.24712769X-RAY DIFFRACTION100
2.4675-2.54010.3221500.22252733X-RAY DIFFRACTION100
2.5401-2.62210.30481500.21962737X-RAY DIFFRACTION100
2.6221-2.71580.29511570.21022734X-RAY DIFFRACTION100
2.7158-2.82450.28151370.212738X-RAY DIFFRACTION100
2.8245-2.95310.29231490.21852762X-RAY DIFFRACTION100
2.9531-3.10870.29781470.2162730X-RAY DIFFRACTION99
3.1087-3.30340.28341450.2032739X-RAY DIFFRACTION99
3.3034-3.55840.23371370.18162746X-RAY DIFFRACTION99
3.5584-3.91630.22711520.14172759X-RAY DIFFRACTION100
3.9163-4.48260.16681540.12872767X-RAY DIFFRACTION99
4.4826-5.6460.16861200.12812776X-RAY DIFFRACTION100
5.646-46.0520.18761550.15512783X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.5617-0.3912-1.01550.94140.05821.03250.10010.44780.1317-0.2257-0.0050.091-0.0087-0.1965-0.07850.301-0.04820.02140.24-0.0310.2482-8.1874-3.933423.3157
21.97970.63830.19261.92310.67430.5478-0.05470.03860.1425-0.003-0.01020.05530.0086-0.07950.06090.18690.01290.00020.19970.020.1837-2.19975.872342.0565
31.73850.2054-0.04681.0140.01694.2410.04520.40080.1884-0.2930.0462-0.1130.020.1083-0.06220.25590.00850.11470.25410.01240.291410.92541.772819.2078
44.6956-1.51951.38093.3139-0.54423.1348-0.1169-0.6414-0.27710.22610.0962-0.04680.11460.16530.0030.26790.10590.10770.37910.10870.209212.59662.613981.2187
52.4435-0.86-0.69513.0224-0.11.2446-0.2609-0.76730.0560.46150.0577-0.48790.10970.38430.15470.46930.18360.04490.46370.03240.202919.5613-0.030185.4923
61.7288-1.11680.10252.48190.34670.9316-0.3304-0.5468-0.19090.24760.0883-0.22060.53250.57930.21050.42710.19120.12760.43540.1010.359216.9206-10.139676.2376
70.6373-0.75760.00462.1514-0.82192.4118-0.021-0.1060.10830.1653-0.0701-0.17870.14450.55620.10320.20840.0450.01690.2401-0.01140.262920.5277-3.090361.5831
82.526-0.492-1.41842.7922-0.49772.8652-0.2419-0.0672-0.2955-0.1782-0.1009-0.07560.61390.21610.2980.36420.0980.07470.23780.02170.288118.4218-11.787454.8588
91.1292-0.2657-0.92413.1407-0.23592.57110.0003-0.12510.12620.1252-0.0402-0.4244-0.16780.2470.04560.15020.0596-0.07660.2976-0.01460.320319.00865.477855.8971
100.8733-0.7395-1.96121.45072.44895.1635-0.3068-0.53120.23830.48160.4725-0.59680.07611.202-0.1750.2744-0.0195-0.06940.4431-0.05390.366822.491715.71259.6871
112.88360.01420.46391.03430.02943.33480.0435-0.21790.45130.08270.0025-0.2384-0.25710.2478-0.00360.27040.03110.04510.1806-0.03410.279110.315813.249971.7531
126.5487-0.38061.73481.52160.19763.715-0.5562-0.66480.85730.21470.198-0.1804-0.3824-0.07410.34150.48850.06960.07850.3075-0.09540.419410.520317.088484.26
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 0:185)
2X-RAY DIFFRACTION2chain 'A' and (resseq 186:376)
3X-RAY DIFFRACTION3chain 'A' and (resseq 377:477)
4X-RAY DIFFRACTION4chain 'B' and (resseq 2:31)
5X-RAY DIFFRACTION5chain 'B' and (resseq 32:120)
6X-RAY DIFFRACTION6chain 'B' and (resseq 121:178)
7X-RAY DIFFRACTION7chain 'B' and (resseq 179:263)
8X-RAY DIFFRACTION8chain 'B' and (resseq 264:302)
9X-RAY DIFFRACTION9chain 'B' and (resseq 303:328)
10X-RAY DIFFRACTION10chain 'B' and (resseq 329:352)
11X-RAY DIFFRACTION11chain 'B' and (resseq 353:445)
12X-RAY DIFFRACTION12chain 'B' and (resseq 446:477)

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